Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.14.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94854	0.671
27DAP/17DAP	1.02215	1
39DAP/27DAP	1.07308	0.899
41DAP/39DAP	1.03598	0.935
42DAP/41DAP	0.96855	1
43DAP/42DAP	1.1231	0.875
47DAP/43DAP	1.15728	0.825
52DAP/47DAP	1.16507	0.828
57DAP/52DAP	0.95329	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16209	0.116
17DAP/reference	1.0768	0.476
27DAP/reference	1.09715	0.559
39DAP/reference	1.23645	0.174
41DAP/reference	1.40676	0.012
42DAP/reference	1.01908	0.707
43DAP/reference	1.06689	0.646
47DAP/reference	0.93782	0.258
52DAP/reference	1.02961	1
57DAP/reference	1.02624	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09842	0.312
27DAP/17DAP	1.11597	0.761
39DAP/27DAP	1.23045	0.12
41DAP/39DAP	0.90493	0.645
42DAP/41DAP	1.04822	1
43DAP/42DAP	1.40718	0.094
47DAP/43DAP	1.15156	0.406
52DAP/47DAP	1.09762	0.696
57DAP/52DAP	1.07447	0.67
57DAP/7DAP	0.89371	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96929	0.55
17DAP/reference	1.12979	0.162
27DAP/reference	1.10662	0.026
39DAP/reference	1.05564	0.634
41DAP/reference	1.14116	0.46
42DAP/reference	1.04469	1
43DAP/reference	0.99567	0.608
47DAP/reference	0.96867	0.671
52DAP/reference	0.97371	0.523
57DAP/reference	0.94198	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11588	0.507
17DAP/reference	1.31848	0.124
27DAP/reference	1.20458	0.111
39DAP/reference	1.1248	0.389
41DAP/reference	1.16982	0.301
42DAP/reference	1.16299	0.317
43DAP/reference	1.37357	0.029
47DAP/reference	1.13078	0.176
52DAP/reference	0.96773	0.433
57DAP/reference	1.06881	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16507	0.356
17DAP/reference	1.16972	0.627
27DAP/reference	1.01509	1
39DAP/reference	1.14862	0.218
41DAP/reference	1.17181	0.734
42DAP/reference	1.12592	0.658
43DAP/reference	0.99271	0.503
47DAP/reference	1.06106	0.934
52DAP/reference	0.95892	0.582
57DAP/reference	1.23388	0.124

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80929	0.787
26DAP/20DAP	1.89018	0.17
34DAP/26DAP	1.60604	0.819
51DAP/34DAP	1.24306	0.759
52DAP/51DAP	1.07034	0.888
53DAP/52DAP	0.82471	0.164
55DAP/53DAP	0.92657	0.698
57DAP/55DAP	1.31246	0.037
62DAP/57DAP	0.9632	0.994
68DAP/62DAP	1.00612	0.914
68DAP/14DAP	0.76068	0.375

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98371	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.97881	0.715
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.06919
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.77032
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08158
IL2-6/WTpooled	0.48718	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.82276	0.418
IL12-4/WTpooled	1.09167	0.737
IL1-4/WTpooled	0.78865	0.699
WT/WTpooled	0.9313	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.90142	0.216

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.76371	0.941
DC3000/delta hrp 6h	0.93413	0.95
DC3000/delta hrp 12h	1.13785	1
DC3000/delta hrp 24h	0.73738	0.079

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94754	0.882
DC3000 delta B/DC3000 delta AB	0.99572	0.916

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.55053	1
Exp 36h	1.41557	1
Exp 60h	0.94891	0.855

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.05001	1
Var 0h	0.94622	1
Var 12h I row2-row1	1.04484	0.544
Var 12h NI row2-row1	1.07346	1
Var 36h I row2-row1	1.10639	1
Var 36h NI row2-row1	1.24303	0.482
Var 60h I row2-row1	1.05988	0.543
Var 60h NI row2-row1	1.05711	1
Time course 0hI-0hNI	0.93596	0.582
Time course 12hI-12hNI	1.00633	0.9
Time course 36hI-36hNI	0.88216	0.102
Time course 60hI-60hNI	0.48867	0.006

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.00281	0.921
transgenic ySAMdc/azygous control (breaker)	1.40703	0.178
transgenic ySAMdc/azygous control (red)	1.14955	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98658	0.534

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02121	1

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16478	1
Manapal/WT (break)	1.68932	0.126
Manapal/WT (red)	1.54813	0.126